He was one of four principal investors that funded Theodore D. Judah's idea of building a railway over the Sierra Nevada from Sacramento, California, to Promontory, Utah.

[citation needed] On September 22, 1854, in New York City, Hopkins married his first cousin, Mary Frances Sherwood.

Mary adopted Timothy Nolan, the adult son of her housekeeper, who took the Hopkins name and was given an administrative position at the Union Pacific Railroad.

The architects were the prominent San Francisco firm of Wright & Sanders and the project manager was architectural engineer William Wallace Barbour Sheldon, who worked for Hopkins under the Southern Pacific Improvement Company.

Sometimes called "Uncle Mark", he was the eldest of the four partners and was well known for his thriftiness (it was said that he knew how to "squeeze 106 cents out of every dollar",[4] a reputation that gained him the post of company treasurer.

Noted American historian Hubert Howe Bancroft quotes Collis Huntington as saying, "I never thought anything finished until Hopkins looked at it".

The unseemly courtship raised eyebrows and questions about the motives of the decorator in the wealthy social circles of San Francisco, but they married in 1887 to begin a six-month grand tour of Europe.

Shortly after their return, Mary executed a new will that explicitly excluded her adopted son Timothy Nolan Hopkins, explaining; "The omission to provide in this will for my adopted son, Timothy Hopkins, is intentional, and not occasioned by accident or mistake", and left her fortunes to her new husband, Edward.

The controversy made good fodder for the press, California papers published stories suggesting that Edward had exploited Mary's interest in spiritualism and falsified records to wrest the estate from her adopted son and defraud business partners.

For the remainder of his life, Edward, increasingly reclusive, continued building castles and estates designed by Henry Vaughan, including Searles Castle in Windham, New Hampshire, (a ¼ replica of Stanton Harcourt Manor in Oxon, England) and Pine Lodge in his hometown of Methuen, Massachusetts.